David Cameron's experiment with "two heads are better than one" at the top of Whitehall may not have much longer to run. Rumour has it that Sir Bob Kerslake, head of the civil service in partnership with Sir Jeremy Heywood as cabinet secretary, will soon bow out. Heywood would then assume the panoply of functions enjoyed by their predecessor Lord Gus O'Donnell.

Even now, Heywood is line manager to half the permanent secretaries and, as far as Number 10 and the security apparatus goes, has big executive responsibilities. In most lights, he looks like a generic public manager, sharing at least some of his genes with NHS executives, local authority chiefs and his Whitehall comrades in arms.

But the cabinet secretary's job description also contains peculiar wording. It goes something like this: When ministers are especially embarrassed and haven't got the will (guts?) to do the dirty work themselves, the cabinet secretary will do the honours.

Blair's Labour predecessor Harold Wilson was not averse to using the Whitehall machine, through the agency of his cabinet secretaries, to manage fractious political colleagues and under Margaret Thatcher, Robin Butler sometimes had a role akin to picking up the empties after a night of binge drinking. His predecessor, Robert Armstrong, became a minor celebrity when he biffed a press photographer on his way to an Australian court appearance, trying to suppress the memoirs of the rogue MI5 officer Peter Wright.

So the role of Heywood as supervisor of the smashing of the Guardian hard drives isn't without precedent. On the grounds that neither Theresa May (responsible for MI5) nor William Hague (MI6) themselves wanted to phone up Alan Rusbridger and threaten him with the heavy mob, who else but Heywood?

So one moment Whitehall's top manager is busying himself with organisation charts, recruitment briefs, budgets and normal executive concerns. The next he is engaged in brute politics, metaphorically holding a gun to a newspaper editor's head. It sounds dissonant and is.

The tension between being the politicians' trusty gofer and being the head of a sprawling organisation in much need of managerial modernisation was precisely the reason Cameron (and he wasn't the first prime minister to consider the move) split the jobs of cabinet secretary and head of the civil service. The perception that Kerslake hasn't measured up to the latter isn't the point: the functions of political hatchet man and chief executive of the civil service are distinct and possibly incompatible.

The British system has devised ways of coping with the tension between politics and bureaucracy. In local government, the role of head of paid service and monitoring office, based in statute, put formal space between the official and the political spheres.

In Whitehall, the doctrine of the accounting officer allows permanent secretaries to demand from ministers a written instruction in cases where officials fear they are being given political tasks.

Of course, in practice, council chief executives negotiate between officialdom and councillors without formality; in local authorities with no overall control, the chief executive can get deeply involved in making the political system work.

For doctrinal cover, Heywood may just be relying on "national security" and historical intimacy between the cabinet secretary and the heads of the security and secret intelligence services. Yet, they too have to be managed and should be subject to the disciplines of economy and effectiveness – in other words to organisational rationality. Heywood's role in persecuting the Guardian has pushed him deep into territory where the norms of accountability and efficiency that apply elsewhere seem not to apply.

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